adjLDStat: Check concordance between marker effect and sparse LD matrix.

In psoerensen/qgg: Statistical Tools for Quantitative Genetic Analyses

Check concordance between marker effect and sparse LD matrix.

Description

Check concordance between predicted and observed marker effect. Marker effect is predicted based on sparse LD matrix in Glist.

Usage

adjLDStat(
  stat = NULL,
  Glist = NULL,
  chr = NULL,
  region = NULL,
  msize = NULL,
  threshold = 1e-05,
  overlap = NULL,
  niter = 5
)

Arguments

stat	data frame with marker summary statistics (see required format above)
Glist	list of information about genotype matrix stored on disk
chr	chromosome for which marker effect is checked
region	genome region (in base pairs) for which marker effect is checked
msize	is the number of markers used in the prediction
threshold	p-value threshold used for chisquare test for difference between observed and predicted marker effects
overlap	is the number of markers overlapping between adjacent genome region
niter	is the number of iteration used for detecting outliers

psoerensen/qgg documentation built on March 9, 2024, 10:02 p.m.